Contacts of the helix formed by residues 298 - 310 (chain B) in PDB entry 4J1O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 298 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.1 1.0 - - - +
48B GLU* 3.0 15.4 + - - +
297B GLY* 1.3 71.7 - - - -
299B ASP* 1.3 65.5 + - - -
300B ILE 3.2 3.2 + - - -
302B ALA* 3.0 26.4 + - - +
327B ILE* 4.0 14.9 - - - +
331B TYR* 3.6 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLY* 1.3 70.8 - - - -
300B ILE* 1.3 57.1 + - - +
302B ALA* 4.0 4.4 - - - +
303B ALA* 2.9 32.1 + - - +
324B GLN* 5.8 0.7 - - - +
330B PRO* 3.7 8.8 - - - +
331B TYR* 2.9 27.4 + - + +
332B ASP 2.9 29.1 + - - +
336B GLY* 3.4 16.4 - - - -
337B ILE* 3.0 29.0 + - - +
354B ILE* 3.9 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.1 15.3 - - + -
46B TRP* 3.5 51.8 - - + +
47B GLY* 3.5 28.9 - - - +
48B GLU* 3.3 7.5 + - + +
106B ILE* 4.5 2.5 - - + -
298B GLY 3.3 1.0 - - - -
299B ASP* 1.3 75.3 - - - +
301B ILE* 1.3 67.1 + - - +
303B ALA* 3.8 3.4 - - - +
304B ALA* 3.1 21.1 + - - +
331B TYR* 4.0 20.2 - - + -
352B LEU* 4.1 11.8 - - + +
354B ILE* 4.5 14.8 - - + -
356B PRO* 4.2 10.5 - - + -
361B PHE* 4.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 3.0 39.4 + - + +
49B THR* 5.6 0.9 - - - -
50B CYS* 5.6 1.1 - - + +
106B ILE* 3.6 28.7 - - + -
267B LEU* 4.1 9.2 - - + -
268B THR* 4.0 6.5 - - + -
294B ASP* 3.6 39.5 - - + +
296B TRP 3.6 21.3 - - - +
297B GLY* 3.6 10.8 - - - +
298B GLY 3.5 9.9 - - - +
300B ILE* 1.3 76.3 - - - +
302B ALA* 1.3 67.1 + - - +
304B ALA* 3.2 2.7 + - - -
305B CYS* 3.0 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLY 4.8 3.8 - - - +
298B GLY 3.0 22.2 + - - +
299B ASP 4.0 0.9 - - - +
301B ILE* 1.3 78.8 - - - +
303B ALA* 1.3 57.1 + - - +
305B CYS* 3.3 5.8 + - - +
306B THR* 2.8 32.6 + - - -
322B VAL* 3.8 28.7 - - + +
324B GLN* 6.1 2.2 - - + +
337B ILE* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP 2.9 20.5 + - - +
300B ILE 3.8 3.4 - - - +
302B ALA* 1.3 73.5 - - - +
304B ALA* 1.3 60.8 + - - +
306B THR* 3.2 1.6 + - - -
307B HIS* 2.9 37.6 + - + -
337B ILE* 3.6 18.8 - - + +
352B LEU* 3.9 17.3 - - + +
354B ILE* 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 3.8 30.5 - - + -
267B LEU* 3.6 19.1 - - + -
273B LEU* 3.7 10.9 - - + +
300B ILE 3.1 13.3 + - - +
301B ILE 3.5 7.9 - - - +
303B ALA* 1.3 76.9 - - - +
305B CYS* 1.3 61.8 + - - +
307B HIS* 3.3 3.0 + - - +
308B ILE* 3.2 23.4 + - - +
352B LEU* 3.8 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.1 13.7 - - - -
292B CYS* 3.7 15.1 - - - +
293B ASP* 3.4 33.4 - - - -
294B ASP* 3.9 12.8 - - - -
301B ILE* 3.0 20.5 + - - -
302B ALA* 3.6 9.0 - - - +
304B ALA* 1.3 76.7 - - - +
306B THR* 1.3 58.6 + - - +
308B ILE* 3.3 10.5 - - - +
309B GLY* 2.9 25.5 + - - -
320B VAL* 3.8 13.8 - - + +
321B TRP 5.0 3.4 - - - +
322B VAL* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 4.1 14.4 - - + +
302B ALA 2.8 20.8 + - - -
303B ALA 3.2 4.4 + - - -
305B CYS* 1.3 75.3 - - - +
307B HIS* 1.3 59.1 + - - +
309B GLY* 3.3 0.5 + - - -
310B ALA* 2.9 29.3 + - - +
320B VAL* 3.9 15.9 - - - +
322B VAL* 4.6 0.2 - - - +
337B ILE* 3.7 18.2 - - + +
344B ILE* 3.8 28.6 - - + +
346B LEU* 3.7 26.7 - - + -
347B PRO* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG* 4.1 15.3 - - + -
120B VAL* 3.7 19.7 + - + -
121B ALA* 3.0 47.3 + - - +
124B LEU* 4.8 0.4 - - + -
303B ALA* 2.9 31.8 + - + +
304B ALA 3.8 5.2 - - - +
305B CYS 3.3 0.2 - - - -
306B THR* 1.3 76.0 - - - +
308B ILE* 1.3 62.7 + - - +
310B ALA* 3.3 7.8 + - - +
311B THR* 3.5 4.9 - - - +
346B LEU* 3.7 26.8 - - + +
347B PRO* 4.3 5.4 - - + +
349B GLY 5.1 0.2 - - - -
351B GLY 3.5 18.4 - - - -
352B LEU* 2.9 36.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.0 19.0 - - + +
267B LEU* 4.8 3.1 - - + -
273B LEU* 3.9 15.7 - - + +
276B MET* 3.7 27.6 - - + +
277B ALA* 4.0 22.4 - - + +
280B ARG* 3.8 20.9 - - + +
292B CYS* 3.9 20.0 - - + -
304B ALA 3.2 10.0 + - - +
305B CYS* 3.3 15.3 - - - +
307B HIS* 1.3 77.6 - - - +
309B GLY* 1.3 66.0 + - - +
311B THR* 2.7 38.5 + - - +
312B VAL* 3.6 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.8 6.4 - - - +
292B CYS* 3.9 13.2 - - - -
305B CYS 2.9 17.9 + - - -
306B THR 3.3 2.0 + - - -
308B ILE* 1.3 76.8 - - - +
310B ALA* 1.3 60.0 + - - +
311B THR 3.2 1.2 + - - -
312B VAL* 3.2 11.4 + - - +
317B ASN* 3.1 22.6 + - - -
320B VAL* 3.9 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ALA* 4.4 4.3 - - + -
126B GLY 4.5 0.2 - - - -
127B VAL* 4.6 2.0 - - + -
128B ALA* 2.8 33.9 + - - +
129B ALA* 3.3 23.5 + - - +
132B VAL* 3.6 14.3 - - + +
306B THR 2.9 17.1 + - - +
307B HIS 3.6 6.5 - - - +
308B ILE 3.2 0.8 - - - -
309B GLY* 1.3 75.8 - - - +
311B THR* 1.3 53.4 + - - +
312B VAL 3.4 0.9 - - - -
346B LEU* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il